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I have no idea how to reproduce it, it just... happens. I've experienced it since ~0.3.7, and it's extremely rare, but OCCASIONALLY, Famitracker will skip frames of a song when you switch songs in a module. I do know one thing about it, it has something to do with the bottoms of frames.
I have very little idea what could cause this, so, if I were daft and daring, I'd say it MIGHT be messy code, but, while I joke about them on occasion, I'm not wishing to start a scorching struggle.
I'd say that, with it's link to the bottom of the frame, there might be a point in the frame where a switch of songs will not properly reset the cursor position, but I have no idea what could cause that.